Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
Thanks You all. Mark you were right. Some how mpi was screwed up. Now I am able to run the job parallely. Actually there were two different versions of openmpi and I suppose they were conflicting. Uninstalling both of them and instally the recent openmpi solved the problem Chandan -- Chandan kumar Choudhury NCL, Pune INDIA On Mon, Feb 1, 2010 at 5:02 PM, Mark Abraham wrote: > On 01/02/10 20:19, Sarath Kumar wrote: > >> >> >>Message: 2 >>Date: Mon, 1 Feb 2010 12:31:32 +0530 >>From: Chandan Choudhury mailto:iitd...@gmail.com>> >> >> Subject: Re: [gmx-users] error: Cannot compile and link MPI code with >>mpicc >>To: Discussion list for GROMACS users ><mailto:gmx-users@gromacs.org>> >> >>Message-ID: >><4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com >><mailto:4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com>> >> >>Content-Type: text/plain; charset="iso-8859-1" >> >>Thanks. >>I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc >>file, and could compile the mpi version of gromacs. >>The next thing is I got the error on executing mdrun_mpi -h >>Following is the output. Kindly help. >> >>corsica:/usr/local/gromacs/bin # mdrun_mpi -h >>[corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file >>runtime/orte_init_stage1.c at line 182 >> >> -- >>It looks like orte_init failed for some reason; your parallel process >> is >>likely to abort. There are many reasons that a parallel process can >>fail during orte_init; some of which are due to configuration or >>environment problems. This failure appears to be an internal failure; >>here's some additional information (which may only be relevant to an >>Open MPI developer): >> >> orte_rml_base_select failed >> --> Returned value -13 instead of ORTE_SUCCESS >> >> >> -- >> >> -- >>It looks like MPI_INIT failed for some reason; your parallel process is >>likely to abort. There are many reasons that a parallel process can >>fail during MPI_INIT; some of which are due to configuration or >>environment >>problems. This failure appears to be an internal failure; here's some >>additional information (which may only be relevant to an Open MPI >>developer): >> >> ompi_mpi_init: orte_init_stage1 failed >> --> Returned "Not found" (-13) instead of "Success" (0) >> >> -- >>*** An error occurred in MPI_Init >>*** before MPI was initialized >>*** MPI_ERRORS_ARE_FATAL (goodbye) >>[corsica:17130] Abort before MPI_INIT completed successfully; not >>able to >>guarantee that all other processes were killed! >> >>-- >>Chandan kumar Choudhury >>NCL, Pune >>INDIA >> >> >> >> >> U will be getting error s like this >> as the MPI failed. >> When u run mdrun with MPI. >> If u use this CPPFLAGS, and i also had a problem. >> When i used this option, after that i was unable to revert back it to >> the original state also. >> >> So the better option update the gcc, c++ compilers, >> If u have doubt in this, remove gromacs, All MPi. >> >> then do yum install -y *openmpi* >> >> --It will automatically install the missing libraries in dependencies. >> >> and then download fftw ---latest >> >> the install fftw with >> ./configure --enable-threads --enable-mpi >> the gromacs >> ./configure --enable-threads --enable-mpi >> >> >> this will surely work, because in order gromacs work with MPI. >> U should compile fftw with MPI as above. >> > > None of this will help if the MPI environment is not configured, e.g. a > hostfile set up. Chandan needs to get a test MPI program to run before there > is evidence any of this discussion belongs on the GROMACS mailing last. > > Mark > > -- > gmx-users mailing listgmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
On 01/02/10 20:19, Sarath Kumar wrote:
Message: 2
Date: Mon, 1 Feb 2010 12:31:32 +0530
From: Chandan Choudhury mailto:iitd...@gmail.com>>
Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
mpicc
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID:
<4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com
<mailto:4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"
Thanks.
I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc
file, and could compile the mpi version of gromacs.
The next thing is I got the error on executing mdrun_mpi -h
Following is the output. Kindly help.
corsica:/usr/local/gromacs/bin # mdrun_mpi -h
[corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
--
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_rml_base_select failed
--> Returned value -13 instead of ORTE_SUCCESS
--
--
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or
environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: orte_init_stage1 failed
--> Returned "Not found" (-13) instead of "Success" (0)
--
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (goodbye)
[corsica:17130] Abort before MPI_INIT completed successfully; not
able to
guarantee that all other processes were killed!
--
Chandan kumar Choudhury
NCL, Pune
INDIA
U will be getting error s like this
as the MPI failed.
When u run mdrun with MPI.
If u use this CPPFLAGS, and i also had a problem.
When i used this option, after that i was unable to revert back it to
the original state also.
So the better option update the gcc, c++ compilers,
If u have doubt in this, remove gromacs, All MPi.
then do yum install -y *openmpi*
--It will automatically install the missing libraries in dependencies.
and then download fftw ---latest
the install fftw with
./configure --enable-threads --enable-mpi
the gromacs
./configure --enable-threads --enable-mpi
this will surely work, because in order gromacs work with MPI.
U should compile fftw with MPI as above.
None of this will help if the MPI environment is not configured, e.g. a
hostfile set up. Chandan needs to get a test MPI program to run before
there is evidence any of this discussion belongs on the GROMACS mailing
last.
Mark
--
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Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
Message: 2 > Date: Mon, 1 Feb 2010 12:31:32 +0530 > From: Chandan Choudhury > Subject: Re: [gmx-users] error: Cannot compile and link MPI code with > mpicc > To: Discussion list for GROMACS users > Message-ID: ><4e22679c1001312301x5ee854dbn401b1e11f8d4b...@mail.gmail.com> > Content-Type: text/plain; charset="iso-8859-1" > > Thanks. > I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc > file, and could compile the mpi version of gromacs. > The next thing is I got the error on executing mdrun_mpi -h > Following is the output. Kindly help. > > corsica:/usr/local/gromacs/bin # mdrun_mpi -h > [corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file > runtime/orte_init_stage1.c at line 182 > -- > It looks like orte_init failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during orte_init; some of which are due to configuration or > environment problems. This failure appears to be an internal failure; > here's some additional information (which may only be relevant to an > Open MPI developer): > > orte_rml_base_select failed > --> Returned value -13 instead of ORTE_SUCCESS > > -- > -- > It looks like MPI_INIT failed for some reason; your parallel process is > likely to abort. There are many reasons that a parallel process can > fail during MPI_INIT; some of which are due to configuration or environment > problems. This failure appears to be an internal failure; here's some > additional information (which may only be relevant to an Open MPI > developer): > > ompi_mpi_init: orte_init_stage1 failed > --> Returned "Not found" (-13) instead of "Success" (0) > -- > *** An error occurred in MPI_Init > *** before MPI was initialized > *** MPI_ERRORS_ARE_FATAL (goodbye) > [corsica:17130] Abort before MPI_INIT completed successfully; not able to > guarantee that all other processes were killed! > > -- > Chandan kumar Choudhury > NCL, Pune > INDIA > > U will be getting error s like this as the MPI failed. When u run mdrun with MPI. If u use this CPPFLAGS, and i also had a problem. When i used this option, after that i was unable to revert back it to the original state also. So the better option update the gcc, c++ compilers, If u have doubt in this, remove gromacs, All MPi. then do yum install -y *openmpi* --It will automatically install the missing libraries in dependencies. and then download fftw ---latest the install fftw with ./configure --enable-threads --enable-mpi the gromacs ./configure --enable-threads --enable-mpi this will surely work, because in order gromacs work with MPI. U should compile fftw with MPI as above. -- B. Sarath Kumar, B.tech. -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
On 01/02/10 18:01, Chandan Choudhury wrote:
Thanks.
I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc
file, and could compile the mpi version of gromacs.
The next thing is I got the error on executing mdrun_mpi -h
Following is the output. Kindly help.
corsica:/usr/local/gromacs/bin # mdrun_mpi -h
Have you set up your machine to run MPI jobs properly? Read the MPI
library documentation and make a non-GROMACS test case work properly first.
Mark
[corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
--
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_rml_base_select failed
--> Returned value -13 instead of ORTE_SUCCESS
--
--
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: orte_init_stage1 failed
--> Returned "Not found" (-13) instead of "Success" (0)
--
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (goodbye)
[corsica:17130] Abort before MPI_INIT completed successfully; not able
to guarantee that all other processes were killed!
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Feb 1, 2010 at 10:50 AM, Sarath Kumar mailto:bskumar.t...@gmail.com>> wrote:
Message: 5
Date: Sun, 31 Jan 2010 00:34:22 +0530
From: Chandan Choudhury mailto:iitd...@gmail.com>>
Subject: Re: [gmx-users] error: Cannot compile and link MPI code
with
mpicc
To: Discussion list for GROMACS users mailto:gmx-users@gromacs.org>>
Message-ID:
<4e22679c1001301104r5f1d725bjd5824e68cb3cb...@mail.gmail.com
<mailto:4e22679c1001301104r5f1d725bjd5824e68cb3cb...@mail.gmail.com>>
Content-Type: text/plain; charset="iso-8859-1"
Hi Ronald !!
Thanks for your reply.
I recompiled the openmpi. But while executing ./configure
--enable-mpi in
gromacs4.0.7 the following error is shown in config.log file.
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 conftest.c >&5
conftest.c:15:17: error: mpi.h: No such file or directory
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.0.7"
| #define PACKAGE_STRING "gromacs 4.0.7"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org
<mailto:gmx-users@gromacs.org>"
| #define PACKAGE "gromacs"
| #define VERSION "4.0.7"
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME "Mon Feb 1 14:07:34 EST 2010"
| #define BUILD_USER "r...@corsica"
| #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
| /* end confdefs.h. */
| #include
| int
| main ()
| {
| int argc; char **argv; MPI_Init(&argc,&argv);
| ;
| return 0;
| }
configure:4619: error: Cannot compile and link MPI code with mpicc
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Jan 30, 2010 at 10:57 PM, Roland Schulz mailto:rol...@utk.edu>> wrote:
> Hi,
>
> your MPI installation has to be brogen. mpicc always has to
be able to find
> libmpi. Please reinstall mpi correctly.
>
> Roland
>
> On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury
mailto:iitd...@gmail.com>>wrote:
>
>> Hi gmx users !!
>>
Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
Thanks.
I just added export CPPFLAGS=-I/usr/local/openmpi/include in the bashrc
file, and could compile the mpi version of gromacs.
The next thing is I got the error on executing mdrun_mpi -h
Following is the output. Kindly help.
corsica:/usr/local/gromacs/bin # mdrun_mpi -h
[corsica:17130] [NO-NAME] ORTE_ERROR_LOG: Not found in file
runtime/orte_init_stage1.c at line 182
--
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_rml_base_select failed
--> Returned value -13 instead of ORTE_SUCCESS
--
--
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: orte_init_stage1 failed
--> Returned "Not found" (-13) instead of "Success" (0)
--
*** An error occurred in MPI_Init
*** before MPI was initialized
*** MPI_ERRORS_ARE_FATAL (goodbye)
[corsica:17130] Abort before MPI_INIT completed successfully; not able to
guarantee that all other processes were killed!
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Mon, Feb 1, 2010 at 10:50 AM, Sarath Kumar wrote:
>
>
>> Message: 5
>> Date: Sun, 31 Jan 2010 00:34:22 +0530
>> From: Chandan Choudhury
>> Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
>>mpicc
>> To: Discussion list for GROMACS users
>> Message-ID:
>><4e22679c1001301104r5f1d725bjd5824e68cb3cb...@mail.gmail.com>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Hi Ronald !!
>> Thanks for your reply.
>> I recompiled the openmpi. But while executing ./configure --enable-mpi in
>> gromacs4.0.7 the following error is shown in config.log file.
>>
>> configure:4536: checking for mpicc
>> configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
>> configure:4563: result: mpicc
>> configure:4577: checking whether the MPI cc command works
>> configure:4601: mpicc -o conftest -g -O2 conftest.c >&5
>> conftest.c:15:17: error: mpi.h: No such file or directory
>> configure:4607: $? = 1
>> configure: failed program was:
>> | /* confdefs.h. */
>> | #define PACKAGE_NAME "gromacs"
>> | #define PACKAGE_TARNAME "gromacs"
>> | #define PACKAGE_VERSION "4.0.7"
>> | #define PACKAGE_STRING "gromacs 4.0.7"
>> | #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
>> | #define PACKAGE "gromacs"
>> | #define VERSION "4.0.7"
>> | #define GMX_SOFTWARE_SQRT
>> | #define GMX_QMMM_GAUSSIAN
>> | #define BUILD_TIME "Mon Feb 1 14:07:34 EST 2010"
>> | #define BUILD_USER "r...@corsica"
>> | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
>> | /* end confdefs.h. */
>> | #include
>> | int
>> | main ()
>> | {
>> | int argc; char **argv; MPI_Init(&argc,&argv);
>> | ;
>> | return 0;
>> | }
>> configure:4619: error: Cannot compile and link MPI code with mpicc
>>
>>
>> --
>> Chandan kumar Choudhury
>> NCL, Pune
>> INDIA
>>
>>
>> On Sat, Jan 30, 2010 at 10:57 PM, Roland Schulz wrote:
>>
>> > Hi,
>> >
>> > your MPI installation has to be brogen. mpicc always has to be able to
>> find
>> > libmpi. Please reinstall mpi correctly.
>> >
>> > Roland
>> >
>> > On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury > >wrote:
>> >
>> >> Hi gmx users !!
>> >>
>> >> On compiling GMX paralley, following error was encountered. How can I
>> >> tackle this.
>> >> Kindly help.
>> >>
>> >>
>> >> checking for mpicc... mpicc
>> >> checking whether the MPI cc command works... configure: error: Cannot
>> >> compile and link MPI code with mpicc
>> >>
>&g
Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
>
> Message: 5
> Date: Sun, 31 Jan 2010 00:34:22 +0530
> From: Chandan Choudhury
> Subject: Re: [gmx-users] error: Cannot compile and link MPI code with
>mpicc
> To: Discussion list for GROMACS users
> Message-ID:
><4e22679c1001301104r5f1d725bjd5824e68cb3cb...@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi Ronald !!
> Thanks for your reply.
> I recompiled the openmpi. But while executing ./configure --enable-mpi in
> gromacs4.0.7 the following error is shown in config.log file.
>
> configure:4536: checking for mpicc
> configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
> configure:4563: result: mpicc
> configure:4577: checking whether the MPI cc command works
> configure:4601: mpicc -o conftest -g -O2 conftest.c >&5
> conftest.c:15:17: error: mpi.h: No such file or directory
> configure:4607: $? = 1
> configure: failed program was:
> | /* confdefs.h. */
> | #define PACKAGE_NAME "gromacs"
> | #define PACKAGE_TARNAME "gromacs"
> | #define PACKAGE_VERSION "4.0.7"
> | #define PACKAGE_STRING "gromacs 4.0.7"
> | #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
> | #define PACKAGE "gromacs"
> | #define VERSION "4.0.7"
> | #define GMX_SOFTWARE_SQRT
> | #define GMX_QMMM_GAUSSIAN
> | #define BUILD_TIME "Mon Feb 1 14:07:34 EST 2010"
> | #define BUILD_USER "r...@corsica"
> | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
> | /* end confdefs.h. */
> | #include
> | int
> | main ()
> | {
> | int argc; char **argv; MPI_Init(&argc,&argv);
> | ;
> | return 0;
> | }
> configure:4619: error: Cannot compile and link MPI code with mpicc
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Sat, Jan 30, 2010 at 10:57 PM, Roland Schulz wrote:
>
> > Hi,
> >
> > your MPI installation has to be brogen. mpicc always has to be able to
> find
> > libmpi. Please reinstall mpi correctly.
> >
> > Roland
> >
> > On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury >wrote:
> >
> >> Hi gmx users !!
> >>
> >> On compiling GMX paralley, following error was encountered. How can I
> >> tackle this.
> >> Kindly help.
> >>
> >>
> >> checking for mpicc... mpicc
> >> checking whether the MPI cc command works... configure: error: Cannot
> >> compile and link MPI code with mpicc
> >>
> >> The config.log file reads
> >>
> >> configure:4536: checking for mpicc
> >> configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
> >> configure:4563: result: mpicc
> >> configure:4577: checking whether the MPI cc command works
> >> configure:4601: mpicc -o conftest -g -O2 -I/usr/local/openmpi/include/
> >> conftest.c >&5
> >> /usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld:
> >> cannot find -lmpi
> >> collect2: ld returned 1 exit status
> >> configure:4607: $? = 1
> >> configure: failed program was:
> >> | /* confdefs.h. */
> >> | #define PACKAGE_NAME "gromacs"
> >> | #define PACKAGE_TARNAME "gromacs"
> >> #define PACKAGE_VERSION "4.0.7"
> >> | #define PACKAGE_STRING "gromacs 4.0.7"
> >> | #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
> >> | #define PACKAGE "gromacs"
> >> | #define VERSION "4.0.7"
> >> | #define GMX_SOFTWARE_SQRT
> >> | #define GMX_QMMM_GAUSSIAN
> >> | #define BUILD_TIME "Sat Jan 30 21:42:50 IST 2010"
> >> | #define BUILD_USER "r...@shiraz"
> >> | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
> >> | /* end confdefs.h. */
> >> | #include
> >> | int
> >> | main ()
> >> | {
> >> | int argc; char **argv; MPI_Init(&argc,&argv);
> >> | ;
> >> | return 0;
> >> | }
> >> configure:4619: error: Cannot compile and link MPI code with mpicc
> >>
> >>
> >> Chandan
> >>
> >> --
> >> Chandan kumar Choudhury
> >> NCL, Pune
> >> INDIA
> >>
> >> --
>
> **
>
Hi.
If u r using RHL or Fedora series..
Try this before reinstalling openmpi.
Its better to update the Compilers before installing MPI.
I did this in Fedora 10.i386.
yum install -y *gcc*
yum install -y *c++*
Then install open-mpi
as ./configure, make, make install.
If u still have the same problem
error: Cannot compile and link MPI code with mpicc.
Then remove the open-mpi installed folder.
then do yum install -y *open-mpi*
And then try installing gromacs with MPI.
Actually, the first option worked for me.
Also i prefer lam-mpi is the best.
--
B. Sarath Kumar, B.tech.
Anna University, Chennai
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] error: Cannot compile and link MPI code with mpicc
Looks to me like you are not linking properly to the mpi libraries.
Please post your gromacs compilation commands in full. For example,
mine are posted below. Note also that some clusters make it more
difficult for you depending on their setup. I have used clusters in
which the simplest way to ensure access to all of the necessary MPI
libraries is to submit my compilation as a job to the MPI queue.
export FFTW_LOCATION=/scratch/cneale/exe/intel/fftw-3.1.2/exec
export GROMACS_LOCATION=/scratch/cneale/exe/intel/gromacs-4.0.5/exec
export CPPFLAGS="-I$FFTW_LOCATION/include
-I/scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/include
-I/scinet/gpc/mpi/openmpi/1.3.2-intel-v11.0-ofed/lib"
export LDFLAGS=-L$FFTW_LOCATION/lib
./configure --prefix=$GROMACS_LOCATION --without-motif-includes
--without-motif-libraries --without-x --without-xml --enable-mpi
--program-suffix="_openmpi" >output.configure.mpi 2>&1
make >output.make.mpi 2>&1
make install-mdrun >output.make_install.mpi 2>&1
-- original message --
On Sun, Jan 31, 2010 at 12:34 AM, Chandan Choudhury gmail.com>wrote:
Hi Ronald !!
Thanks for your reply.
I recompiled the openmpi. But while executing ./configure --enable-mpi in
gromacs4.0.7 the following error is shown in config.log file.
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 conftest.c >&5
conftest.c:15:17: error: mpi.h: No such file or directory
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.0.7"
| #define PACKAGE_STRING "gromacs 4.0.7"
| #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
| #define PACKAGE "gromacs"
| #define VERSION "4.0.7"
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME "Mon Feb 1 14:07:34 EST 2010"
| #define BUILD_USER "root at corsica"
| #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
| /* end confdefs.h. */
| #include
| int
| main ()
| {
| int argc; char **argv; MPI_Init(&argc,&argv);
| ;
| return 0;
| }
configure:4619: error: Cannot compile and link MPI code with mpicc
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Jan 30, 2010 at 10:57 PM, Roland Schulz wrote:
Hi,
your MPI installation has to be brogen. mpicc always has to be able to
find libmpi. Please reinstall mpi correctly.
Roland
On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury gmail.com>wrote:
Hi gmx users !!
On compiling GMX paralley, following error was encountered. How can I
tackle this.
Kindly help.
checking for mpicc... mpicc
checking whether the MPI cc command works... configure: error: Cannot
compile and link MPI code with mpicc
The config.log file reads
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 -I/usr/local/openmpi/include/
conftest.c >&5
/usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld:
cannot find -lmpi
collect2: ld returned 1 exit status
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
#define PACKAGE_VERSION "4.0.7"
| #define PACKAGE_STRING "gromacs 4.0.7"
| #define PACKAGE_BUGREPORT "gmx-users at gromacs.org"
| #define PACKAGE "gromacs"
| #define VERSION "4.0.7"
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME "Sat Jan 30 21:42:50 IST 2010"
| #define BUILD_USER "root at shiraz"
| #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
| /* end confdefs.h. */
| #include
| int
| main ()
| {
| int argc; char **argv; MPI_Init(&argc,&argv);
| ;
| return 0;
| }
configure:4619: error: Cannot compile and link MPI code with mpicc
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
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865-241-1537, ORNL PO BOX 2008 MS6309
--
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Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
I am using openmpi-1.4.1.
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sun, Jan 31, 2010 at 12:34 AM, Chandan Choudhury wrote:
> Hi Ronald !!
> Thanks for your reply.
> I recompiled the openmpi. But while executing ./configure --enable-mpi in
> gromacs4.0.7 the following error is shown in config.log file.
>
>
> configure:4536: checking for mpicc
> configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
> configure:4563: result: mpicc
> configure:4577: checking whether the MPI cc command works
> configure:4601: mpicc -o conftest -g -O2 conftest.c >&5
> conftest.c:15:17: error: mpi.h: No such file or directory
>
> configure:4607: $? = 1
> configure: failed program was:
> | /* confdefs.h. */
> | #define PACKAGE_NAME "gromacs"
> | #define PACKAGE_TARNAME "gromacs"
> | #define PACKAGE_VERSION "4.0.7"
> | #define PACKAGE_STRING "gromacs 4.0.7"
> | #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
> | #define PACKAGE "gromacs"
> | #define VERSION "4.0.7"
> | #define GMX_SOFTWARE_SQRT
> | #define GMX_QMMM_GAUSSIAN
> | #define BUILD_TIME "Mon Feb 1 14:07:34 EST 2010"
> | #define BUILD_USER "r...@corsica"
>
> | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
> | /* end confdefs.h. */
> | #include
> | int
> | main ()
> | {
> | int argc; char **argv; MPI_Init(&argc,&argv);
> | ;
> | return 0;
> | }
> configure:4619: error: Cannot compile and link MPI code with mpicc
>
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
>
> On Sat, Jan 30, 2010 at 10:57 PM, Roland Schulz wrote:
>
>> Hi,
>>
>> your MPI installation has to be brogen. mpicc always has to be able to
>> find libmpi. Please reinstall mpi correctly.
>>
>> Roland
>>
>> On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury wrote:
>>
>>> Hi gmx users !!
>>>
>>> On compiling GMX paralley, following error was encountered. How can I
>>> tackle this.
>>> Kindly help.
>>>
>>>
>>> checking for mpicc... mpicc
>>> checking whether the MPI cc command works... configure: error: Cannot
>>> compile and link MPI code with mpicc
>>>
>>> The config.log file reads
>>>
>>> configure:4536: checking for mpicc
>>> configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
>>> configure:4563: result: mpicc
>>> configure:4577: checking whether the MPI cc command works
>>> configure:4601: mpicc -o conftest -g -O2 -I/usr/local/openmpi/include/
>>> conftest.c >&5
>>> /usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld:
>>> cannot find -lmpi
>>> collect2: ld returned 1 exit status
>>> configure:4607: $? = 1
>>> configure: failed program was:
>>> | /* confdefs.h. */
>>> | #define PACKAGE_NAME "gromacs"
>>> | #define PACKAGE_TARNAME "gromacs"
>>> #define PACKAGE_VERSION "4.0.7"
>>> | #define PACKAGE_STRING "gromacs 4.0.7"
>>> | #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
>>> | #define PACKAGE "gromacs"
>>> | #define VERSION "4.0.7"
>>> | #define GMX_SOFTWARE_SQRT
>>> | #define GMX_QMMM_GAUSSIAN
>>> | #define BUILD_TIME "Sat Jan 30 21:42:50 IST 2010"
>>> | #define BUILD_USER "r...@shiraz"
>>> | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
>>> | /* end confdefs.h. */
>>> | #include
>>> | int
>>> | main ()
>>> | {
>>> | int argc; char **argv; MPI_Init(&argc,&argv);
>>> | ;
>>> | return 0;
>>> | }
>>> configure:4619: error: Cannot compile and link MPI code with mpicc
>>>
>>>
>>> Chandan
>>>
>>> --
>>> Chandan kumar Choudhury
>>> NCL, Pune
>>> INDIA
>>>
>>> --
>>> gmx-users mailing listgmx-users@gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
>>> posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-requ...@gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>>
>>
>>
>>
>> --
>> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
>> 865-241-1537, ORNL PO BOX 2008 MS6309
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
Hi Ronald !!
Thanks for your reply.
I recompiled the openmpi. But while executing ./configure --enable-mpi in
gromacs4.0.7 the following error is shown in config.log file.
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 conftest.c >&5
conftest.c:15:17: error: mpi.h: No such file or directory
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
| #define PACKAGE_VERSION "4.0.7"
| #define PACKAGE_STRING "gromacs 4.0.7"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE "gromacs"
| #define VERSION "4.0.7"
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME "Mon Feb 1 14:07:34 EST 2010"
| #define BUILD_USER "r...@corsica"
| #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
| /* end confdefs.h. */
| #include
| int
| main ()
| {
| int argc; char **argv; MPI_Init(&argc,&argv);
| ;
| return 0;
| }
configure:4619: error: Cannot compile and link MPI code with mpicc
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Sat, Jan 30, 2010 at 10:57 PM, Roland Schulz wrote:
> Hi,
>
> your MPI installation has to be brogen. mpicc always has to be able to find
> libmpi. Please reinstall mpi correctly.
>
> Roland
>
> On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury wrote:
>
>> Hi gmx users !!
>>
>> On compiling GMX paralley, following error was encountered. How can I
>> tackle this.
>> Kindly help.
>>
>>
>> checking for mpicc... mpicc
>> checking whether the MPI cc command works... configure: error: Cannot
>> compile and link MPI code with mpicc
>>
>> The config.log file reads
>>
>> configure:4536: checking for mpicc
>> configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
>> configure:4563: result: mpicc
>> configure:4577: checking whether the MPI cc command works
>> configure:4601: mpicc -o conftest -g -O2 -I/usr/local/openmpi/include/
>> conftest.c >&5
>> /usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld:
>> cannot find -lmpi
>> collect2: ld returned 1 exit status
>> configure:4607: $? = 1
>> configure: failed program was:
>> | /* confdefs.h. */
>> | #define PACKAGE_NAME "gromacs"
>> | #define PACKAGE_TARNAME "gromacs"
>> #define PACKAGE_VERSION "4.0.7"
>> | #define PACKAGE_STRING "gromacs 4.0.7"
>> | #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
>> | #define PACKAGE "gromacs"
>> | #define VERSION "4.0.7"
>> | #define GMX_SOFTWARE_SQRT
>> | #define GMX_QMMM_GAUSSIAN
>> | #define BUILD_TIME "Sat Jan 30 21:42:50 IST 2010"
>> | #define BUILD_USER "r...@shiraz"
>> | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
>> | /* end confdefs.h. */
>> | #include
>> | int
>> | main ()
>> | {
>> | int argc; char **argv; MPI_Init(&argc,&argv);
>> | ;
>> | return 0;
>> | }
>> configure:4619: error: Cannot compile and link MPI code with mpicc
>>
>>
>> Chandan
>>
>> --
>> Chandan kumar Choudhury
>> NCL, Pune
>> INDIA
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>>
>
>
>
> --
> ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
> 865-241-1537, ORNL PO BOX 2008 MS6309
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] error: Cannot compile and link MPI code with mpicc
Hi,
your MPI installation has to be brogen. mpicc always has to be able to find
libmpi. Please reinstall mpi correctly.
Roland
On Sat, Jan 30, 2010 at 11:06 AM, Chandan Choudhury wrote:
> Hi gmx users !!
>
> On compiling GMX paralley, following error was encountered. How can I
> tackle this.
> Kindly help.
>
>
> checking for mpicc... mpicc
> checking whether the MPI cc command works... configure: error: Cannot
> compile and link MPI code with mpicc
>
> The config.log file reads
>
> configure:4536: checking for mpicc
> configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
> configure:4563: result: mpicc
> configure:4577: checking whether the MPI cc command works
> configure:4601: mpicc -o conftest -g -O2 -I/usr/local/openmpi/include/
> conftest.c >&5
> /usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld: cannot
> find -lmpi
> collect2: ld returned 1 exit status
> configure:4607: $? = 1
> configure: failed program was:
> | /* confdefs.h. */
> | #define PACKAGE_NAME "gromacs"
> | #define PACKAGE_TARNAME "gromacs"
> #define PACKAGE_VERSION "4.0.7"
> | #define PACKAGE_STRING "gromacs 4.0.7"
> | #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
> | #define PACKAGE "gromacs"
> | #define VERSION "4.0.7"
> | #define GMX_SOFTWARE_SQRT
> | #define GMX_QMMM_GAUSSIAN
> | #define BUILD_TIME "Sat Jan 30 21:42:50 IST 2010"
> | #define BUILD_USER "r...@shiraz"
> | #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
> | /* end confdefs.h. */
> | #include
> | int
> | main ()
> | {
> | int argc; char **argv; MPI_Init(&argc,&argv);
> | ;
> | return 0;
> | }
> configure:4619: error: Cannot compile and link MPI code with mpicc
>
>
> Chandan
>
> --
> Chandan kumar Choudhury
> NCL, Pune
> INDIA
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
--
ORNL/UT Center for Molecular Biophysics cmb.ornl.gov
865-241-1537, ORNL PO BOX 2008 MS6309
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
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[gmx-users] error: Cannot compile and link MPI code with mpicc
Hi gmx users !!
On compiling GMX paralley, following error was encountered. How can I tackle
this.
Kindly help.
checking for mpicc... mpicc
checking whether the MPI cc command works... configure: error: Cannot
compile and link MPI code with mpicc
The config.log file reads
configure:4536: checking for mpicc
configure:4552: found /usr/lib/mpi/gcc/openmpi/bin/mpicc
configure:4563: result: mpicc
configure:4577: checking whether the MPI cc command works
configure:4601: mpicc -o conftest -g -O2 -I/usr/local/openmpi/include/
conftest.c >&5
/usr/lib/gcc/i586-suse-linux/4.4/../../../../i586-suse-linux/bin/ld: cannot
find -lmpi
collect2: ld returned 1 exit status
configure:4607: $? = 1
configure: failed program was:
| /* confdefs.h. */
| #define PACKAGE_NAME "gromacs"
| #define PACKAGE_TARNAME "gromacs"
#define PACKAGE_VERSION "4.0.7"
| #define PACKAGE_STRING "gromacs 4.0.7"
| #define PACKAGE_BUGREPORT "gmx-users@gromacs.org"
| #define PACKAGE "gromacs"
| #define VERSION "4.0.7"
| #define GMX_SOFTWARE_SQRT
| #define GMX_QMMM_GAUSSIAN
| #define BUILD_TIME "Sat Jan 30 21:42:50 IST 2010"
| #define BUILD_USER "r...@shiraz"
| #define BUILD_MACHINE "Linux 2.6.31.5-0.1-desktop i686"
| /* end confdefs.h. */
| #include
| int
| main ()
| {
| int argc; char **argv; MPI_Init(&argc,&argv);
| ;
| return 0;
| }
configure:4619: error: Cannot compile and link MPI code with mpicc
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gromacs.org/search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/mailing_lists/users.php
